Genome-wide identification and expression analysis of the MADS gene family in sweet orange (Citrus sinensis) infested with pathogenic bacteria.

The risk of pathogenic bacterial invasion in plantations has increased dramatically due to high environmental climate change and has seriously affected sweet orange fruit quality. MADS genes allow plants to develop increased resistance, but functional genes for resistance associated with pathogen invasion have rarely been reported. MADS gene expression profiles were analyzed in sweet orange leaves and fruits infested with Lecanicillium psalliotae and Penicillium digitatum, respectively. Eighty-two MADS genes were identified from the sweet orange genome, and they were classified into five prime subfamilies concerning the Arabidopsis MADS gene family, of which the MIKC subfamily could be subdivided into 13 minor subfamilies. Protein structure analysis showed that more than 93% of the MADS protein sequences of the same subfamily between sweet orange and Arabidopsis were very similar in tertiary structure, with only CsMADS8 and AG showing significant differences. The variability of MADS genes protein structures between sweet orange and Arabidopsis subgroups was less than the variabilities of protein structures within species. Chromosomal localization and covariance analysis showed that these genes were unevenly distributed on nine chromosomes, with the most genes on chromosome 9 and the least on chromosome 2, with 36 and two, respectively. Four pairs of tandem and 28 fragmented duplicated genes in the 82 MADS gene sequences were found in sweet oranges. GO (Gene Ontology) functional enrichment and expression pattern analysis showed that the functional gene CsMADS46 was strongly downregulated of sweet orange in response to biotic stress adversity. It is also the first report that plants' MADS genes are involved in the biotic stress responses of sweet oranges. For the first time, L. psalliotae was experimentally confirmed to be the causal agent of sweet orange leaf spot disease, which provides a reference for the research and control of pathogenic L. psalliotae.

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum.

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis).

BACKGROUND: The NBS-LRR (nucleotide-binding site-leucine-rich repeat gene) gene family, known as the plant R (resistance) gene family with the most members, plays a significant role in plant resistance to various external adversity stresses. The NBS-LRR gene family has been researched in many plant species. Citrus is one of the most vital global cash crops, the number one fruit group, and the third most traded agricultural product world wild. However, as one of the largest citrus species, a comprehensive study of the NBS-LRR gene family has not been reported on sweet oranges. METHODS: In this study, NBS-LRR genes were identified from the Citrus sinensis genome (v3.0), with a comprehensive analysis of this gene family performed, including phylogenetic analysis, gene structure, cis-acting element of a promoter, and chromosomal localization, among others. The expression pattern of NBS-LRR genes was analyzed when sweet orange fruits were infected by Penicillium digitatum, employing experimental data from our research group. It first reported the expression patterns of NBS-LRR genes under abiotic stresses, using three transcript data from NCBI (National Center for Biotechnology Information). RESULTS: In this study, 111 NBS-LRR genes were identified in the C. sinensis genome (v3.0) and classified into seven subfamilies according to their N-terminal and C-terminal domains. The phylogenetic tree results indicate that genes containing only the NBS structural domain are more ancient in the sweet orange NBS-LRR gene family. The chromosome localization results showed that 111 NBS-LRR genes were distributed unevenly on nine chromosomes, with the most genes distributed on chromosome 1. In addition, we identified a total of 18 tandem duplication gene pairs in the sweet orange NBS-LRR gene family, and based on the Ka/Ks ratio, all of the tandem duplication genes underwent purifying selection. Transcriptome data analysis showed a significant number of NBS-LRR genes expressed under biotic and abiotic stresses, and some reached significantly different levels of expression. It indicates that the NBS-LRR gene family is vital in resistance to biotic and abiotic stresses in sweet oranges. CONCLUSION: Our study provides the first comprehensive framework on the NBS-LRR family of genes, which provides a basis for further in-depth studies on the biological functions of NBS-LRR in growth, development, and response to abiotic stresses in sweet orange.